The present study attempted estimations of watershed-scale storage changes at two mountainous watersheds in northern Thailand to understand the behaviors of watershed-scale storage under the 2011 Chao Phraya River flood. For this purpose, we applied a methodology that separates an hourly hydrograph into several discharge sub-components, and formulized watershed-scale storage-discharge relationships. The results showed that (1) this methodology was applicable to sub-tropic watersheds, (2) there were five different discharge sub-components, that correspond to the number of dominant rainfall-runoff processes, in two mountainous watersheds in northern Thailand, (3) the peak total storage in 2011 was estimated to occur in October because of strongly seasonal slower discharge sub-components, whereas the maximum total discharge was observed in June, (4) the sum of watershed-scale maximum storages of all the discharge sub-components in the upper Yom and Nan River watersheds were respectively estimated to be 135 mm and 405 mm, and the difference might be explained by the existence of the active fault running north-south in the upper Nan River watershed, and (5) the estimated storage with the recession time constants of 111 h at the beginnings of rainy seasons could explain the risk of slope failure occurrences within a watershed.